Energy consumption in the Chinese rural areas features massive use of low-grade energy commodities and the distempered structure of exorbitant leaning on biomass energy. This has provoked an increasingly exacerbating environment and exerted a depressing effect on agriculturally sustainable development. Pilot energy engineering practices of efficient utilization environment improvement have seen a surge on a vast extent of rural lands. As a typical engineering of energy resources for methane production, the four-dimension-inone-geometry model concerning ecological agriculture has triggered scholarly attention. The aim of this study is to deal with energy flows in this system whereby to put forward measures for its upgrading and ultimately offer policies for rural energy development and use. First, the study depicts the models structure and working process, and the methodology of estimating its energy flows. Next, taking a three member household as an example, the study estimates the quantity in its energy flows, finding that the whole system imports 1,195,102 MJ of energy and generates 35,728MJ, with 47.3% yielded by the breeding system, 32.1% by the anaerobic fermentation system, and 20.6% by the planting system. Comparatively, this model has neither achieved the artificially auxiliary energy-output ratio of 2.4:1, a criterion for high yield, nor reached the national high output standard of 38.1GJ/hm2 in inorganic energy investment and the height of 124.3 GJ/hm2 of farmland energy input in the bio-energy zones of good harvest. On this ground, this study presents countermeasures to further improve the models energy efficiency and strategies related to rural energy development. Those suggestions might apply to other rural areas.